Photoshop: Edge pixels are duplicated when transforms don't land on pixel boundaries

I drew this + shape to a new unfilled layer. (the image here is zoomed in at 1600%, the colored squares are one pixel each)
If I zoom to 200%, Cmd-T to invoke transform mode, then nudge once to the right, and once down, and commit the transform by pressing enter, I get the second image here as a result. The left and top pixels are removed, and the bottom and right pixels are duplicated. The interior pixels are not changed.

The transform has to land perfectly between pixels for this to happen. It happens by chance quite often when I am using smart objects. Scaling can also cause the issue.

If you are on a fractional boundary (not on exact pixel boundaries) -- what you showed is entirely expected. The location of the resampled pixels fall on fractional locations, which will be interpolated, and in some cases repeat edge pixels to deal with interpolated values from outside the original sample bounds (because the interpolation has a non-zero width).

If you want pixel perfect transforms, you need to make sure that your transform bounds fall on pixel boundaries - which is what the preference in CS6 is designed to do.

Again, ALL the pixels follow the same rules for resampling. But the edge pixels have to be replicated to handle the edges (because there is nothing beyond the edges). Translating it up and left by 0.5 pixels would produce exactly what you show.

I've run into a very similar issue even when the pixel snapping preference is on.
The image on the left is the smart object scaled down in a document, the image on the right is the contents of the smart object.
In the first group, some of the antialiasing is cut off (along the top, bottom, left and right). In the second version I just drew the two small blue dots inside the smart object. The antialiasing on the big circle has now returned.

Because the edges were snapped to pixel boundaries. the antialiasing isn't necessarily cut off so much as reduced because the edges of the shape fall on pixel boundaries -- which is exactly what UI designers asked for in that feature.